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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgacgaagcacctgatcaaaccaactcaacctctcatcaaagtatctctgaaattcccggctaatacagttggttctctcttgatctgctgcag

Basic information

species Zea mays
transcript GRMZM2G141399_T01
intron # 13
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|67021517|gb|CO450266.1|CO450266
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|31352858|gb|CD437215.1|CD437215
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|32835013|gb|CD974691.1|CD974691
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|13149461|gb|BG319783.1|BG319783
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGA-CCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|32833105|gb|CD972783.1|CD972783
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|67014870|gb|CO443619.1|CO443619
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|24764332|gb|CA399497.1|CA399497
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|31351712|gb|CD436069.1|CD436069
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|24769423|gb|CA404552.1|CA404552
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTG
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 36 (upstream exon), 46 (downstream exon)
Score: 41

AATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGCGGCCTAACTCAGCTCGTCGCCATGCGGTATGGGACCATCCCGATTGTCC


Block sizes: 48 (upstream exon), 18 (downstream exon)
Score: 4

AATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGCGGCCTAACTCAGCTCGTCGCCATGCGGTATGGGACCATCCCGATTGTCC


Block sizes: 36 (upstream exon), 45 (downstream exon)
Score: 4

AATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGCGGCCTAACTCAGCTCGTCGCCATGCGGTATGGGACCATCCCGATTGTCC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 40

AATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGCGGCCTAACTCAGCTCGTCGCCATGCGGTATGGGACCATCCCGATTGTCC